Index

A

AccessionNumber (spydcmtk.dcmTools.DicomTags attribute) AcquisitionMatrix (spydcmtk.dcmTools.DicomTags attribute) addFieldDataFromDcmDataSet() (in module spydcmtk.dcmVTKTK) anat (spydcmtk.dcmTK.BIDSConst attribute) anonymise() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method)

anonymiseDicomDS() (in module spydcmtk.dcmTools) anonymiseInPlace() (in module spydcmtk.spydcm) array_to_DcmSeg() (in module spydcmtk.dcmVTKTK) arrToVTI() (in module spydcmtk.dcmVTKTK) arrToVTS() (in module spydcmtk.dcmVTKTK)

B

BIDS_Directory (class in spydcmtk.dcmTK) BIDS_Subject (class in spydcmtk.dcmTK) BIDSConst (class in spydcmtk.dcmTK) BodyPartExamined (spydcmtk.dcmTools.DicomTags attribute) buildFakeDS() (in module spydcmtk.dcmTools) buildFDQ() (spydcmtk.spydcm.INTERACTIVE method) buildImage2PatientCoordinateMatrix() (spydcmtk.dcmVTKTK.PatientMeta method)

buildMSTable() (spydcmtk.dcmTK.ListOfDicomStudies method) buildOverviewImage() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.spydcm.INTERACTIVE method) buildTableOfDicomParamsForManuscript() (in module spydcmtk.spydcm) buildVTIDict() (spydcmtk.dcmTK.DicomSeries method) buildVTS() (spydcmtk.spydcm.INTERACTIVE method) buildVTSDict() (spydcmtk.dcmTK.DicomSeries method)

C

CardiacNumberOfImages (spydcmtk.dcmTools.DicomTags attribute) checkArgs() (in module spydcmtk.spydcm) checkIfShouldUse_SAFE_NAMING() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method)

cleanString() (in module spydcmtk.dcmTools) code (spydcmtk.dcmTK.BIDSConst attribute) configf (spydcmtk.dcmTK.BIDSConst attribute) convertInputsToHTML() (in module spydcmtk.spydcm) countFilesInDir() (in module spydcmtk.dcmTools)

D

dataSummary() (spydcmtk.spydcm.INTERACTIVE method) dbDateToDateTime() (in module spydcmtk.dcmTools) default() (spydcmtk.dcmTools.NumpyEncoder method) DicomSeries (class in spydcmtk.dcmTK) DicomStudy (class in spydcmtk.dcmTK) DicomTags (class in spydcmtk.dcmTools) Dimensions (spydcmtk.dcmVTKTK.PatientMeta property)

directoryToVTI() (in module spydcmtk.spydcm) directoryToVTS() (in module spydcmtk.spydcm) displayMenu() (spydcmtk.spydcm.INTERACTIVE method) distBetweenTwoPts() (in module spydcmtk.dcmTK) distPts() (in module spydcmtk.dcmTools) doesSliceLocationNorm_Match_IOPNormal() (spydcmtk.dcmTK.DicomSeries method) dwi (spydcmtk.dcmTK.BIDSConst attribute)

E

EchoTime (spydcmtk.dcmTools.DicomTags attribute)

error() (spydcmtk.spydcm.MyParser method)

F

filterByTag() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method) filterResampleToImage() (in module spydcmtk.dcmVTKTK)

fixPath() (in module spydcmtk.dcmTools) FlipAngle (spydcmtk.dcmTools.DicomTags attribute) fmap (spydcmtk.dcmTK.BIDSConst attribute) func (spydcmtk.dcmTK.BIDSConst attribute)

G

getAllDirsUnderRootWithDicoms() (in module spydcmtk.spydcm) getConfigFile() (spydcmtk.dcmTK.BIDS_Directory method) getDcmSeg_meta_depreciated() (in module spydcmtk.dcmVTKTK) getDeltaCol() (spydcmtk.dcmTK.DicomSeries method) getDeltaRow() (spydcmtk.dcmTK.DicomSeries method) getDeltaSlice() (spydcmtk.dcmTK.DicomSeries method) getDicomDictFromTar() (in module spydcmtk.dcmTools) getDicomDictFromZip() (in module spydcmtk.dcmTools) getDicomFileIdentifierStr() (in module spydcmtk.dcmTools) getDicomFullFileName() (spydcmtk.dcmTK.DicomSeries method) getDicomTagsDict() (in module spydcmtk.dcmTools) getImageOrientationPatient_np() (spydcmtk.dcmTK.DicomSeries method) getImagePositionPatient_np() (spydcmtk.dcmTK.DicomSeries method) getInternalPulseSequenceName() (spydcmtk.dcmTK.DicomSeries method) getJsonDict() (in module spydcmtk.dcmTK) getManufacturer() (spydcmtk.dcmTK.DicomSeries method) getMatrix() (spydcmtk.dcmVTKTK.PatientMeta method) getMeta() (spydcmtk.dcmVTKTK.PatientMeta method) getMetaForDICOM() (spydcmtk.dcmVTKTK.PatientMeta method) getMetaForVTK() (spydcmtk.dcmVTKTK.PatientMeta method) getNIIMatchingModality() (spydcmtk.dcmTK.BIDS_Subject method) getNIIMatchingModality_condition() (spydcmtk.dcmTK.BIDS_Subject method) getNumberOfDicoms() (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method) getNumberOfSlicesPerVolume() (spydcmtk.dcmTK.DicomSeries method) getNumberOfTimeSteps() (spydcmtk.dcmTK.DicomSeries method) getPatientDirName() (in module spydcmtk.dcmTools) getPatientOverview() (spydcmtk.dcmTK.DicomStudy method) getPixelDataAsNumpy() (spydcmtk.dcmTK.DicomSeries method) getPulseSequenceName() (spydcmtk.dcmTK.DicomSeries method) getResolution() (in module spydcmtk.dcmTK) getRootDir() (spydcmtk.dcmTK.DicomSeries method) getRootDirWithSEdirs() (in module spydcmtk.dcmTools) getSaveFileNameFor_ds() (in module spydcmtk.dcmTools) getSaveFileNameFor_ds_UID() (in module spydcmtk.dcmTools) getScanDuration_secs() (spydcmtk.dcmTK.DicomSeries method) getSeriesByID() (spydcmtk.dcmTK.DicomStudy method) getSeriesBySeriesNumber() (spydcmtk.dcmTK.DicomStudy method) getSeriesByTag() (spydcmtk.dcmTK.DicomStudy method) getSeriesByUID() (spydcmtk.dcmTK.DicomStudy method)

getSeriesDescription() (spydcmtk.dcmTK.DicomSeries method) getSeriesDirName() (in module spydcmtk.dcmTools) getSeriesInfoDict() (spydcmtk.dcmTK.DicomSeries method) getSeriesMatchingDescription() (spydcmtk.dcmTK.DicomStudy method) getSeriesNumber() (spydcmtk.dcmTK.DicomSeries method) getSeriesOutDirName() (spydcmtk.dcmTK.DicomSeries method) getSeriesOverview() (spydcmtk.dcmTK.DicomSeries method) getSeriesTimeAsDatetime() (spydcmtk.dcmTK.DicomSeries method) getSessionDir() (spydcmtk.dcmTK.BIDS_Subject method) getSliceNormalVector() (spydcmtk.dcmTK.DicomSeries method) getStdDicomTags() (in module spydcmtk.dcmTools) getStudyByDate() (spydcmtk.dcmTK.ListOfDicomStudies method) getStudyByPID() (spydcmtk.dcmTK.ListOfDicomStudies method) getStudyByTag() (spydcmtk.dcmTK.ListOfDicomStudies method) getStudyDirName() (in module spydcmtk.dcmTools) getStudyOutputDir() (spydcmtk.dcmTK.DicomSeries method) getStudyOverview() (spydcmtk.dcmTK.DicomStudy method) getStudySummary() (spydcmtk.dcmTK.DicomStudy method) getStudySummaryDict() (spydcmtk.dcmTK.DicomStudy method) getSubjID() (spydcmtk.dcmTK.BIDS_Subject method) getSubjList() (spydcmtk.dcmTK.BIDS_Directory method) getSummaryString() (spydcmtk.dcmTK.ListOfDicomStudies method) getTableOfTagValues() (spydcmtk.dcmTK.ListOfDicomStudies method) getTag() (in module spydcmtk.spydcm) (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) getTagCode() (in module spydcmtk.dcmTools) getTagFromJson() (in module spydcmtk.dcmTK) getTagListAndNames() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) getTagObj() (spydcmtk.dcmTK.DicomSeries method) getTagValuesList() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) getTemporalResolution() (spydcmtk.dcmTK.DicomSeries method) getTemporalResolution_TR_VPS() (spydcmtk.dcmTK.DicomSeries method) getTopDir() (spydcmtk.dcmTK.DicomStudy method) getTypeDir() (spydcmtk.dcmTK.BIDS_Subject method) getUserInput() (spydcmtk.spydcm.INTERACTIVE method) getVENC() (spydcmtk.dcmTK.DicomSeries method) getVtkMatrix() (spydcmtk.dcmVTKTK.PatientMeta method) getVTKTransform() (spydcmtk.dcmVTKTK.PatientMeta method)

H

HeartRate (spydcmtk.dcmTools.DicomTags attribute)

I

ImageOrientationPatient (spydcmtk.dcmTools.DicomTags attribute) (spydcmtk.dcmVTKTK.PatientMeta property) ImagePositionPatient (spydcmtk.dcmTools.DicomTags attribute) (spydcmtk.dcmVTKTK.PatientMeta property) imageToPatientCoordinates() (spydcmtk.dcmVTKTK.PatientMeta method) initFromDicomSeg() (spydcmtk.dcmVTKTK.PatientMeta method) initFromDicomSeries() (spydcmtk.dcmVTKTK.PatientMeta method) initFromDictionary() (spydcmtk.dcmVTKTK.PatientMeta method) initFromVTI() (spydcmtk.dcmVTKTK.PatientMeta method) inspect() (in module spydcmtk.spydcm) InstanceNumber (spydcmtk.dcmTools.DicomTags attribute)

instanceNumberSortKey() (in module spydcmtk.dcmTools) INTERACTIVE (class in spydcmtk.spydcm) InversionTime (spydcmtk.dcmTools.DicomTags attribute) is3D() (spydcmtk.dcmTK.DicomSeries method) is4D() (spydcmtk.dcmTK.DicomSeries method) IS_BRUKER() (spydcmtk.dcmTK.DicomSeries method) IS_GE() (spydcmtk.dcmTK.DicomSeries method) IS_PHILIPS() (spydcmtk.dcmTK.DicomSeries method) IS_SIEMENS() (spydcmtk.dcmTK.DicomSeries method) isCompressed() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method)

L

ListOfDicomStudies (class in spydcmtk.dcmTK)

M

MagneticFieldStrength (spydcmtk.dcmTools.DicomTags attribute) main() (in module spydcmtk.spydcm) Manufacturer (spydcmtk.dcmTools.DicomTags attribute) ManufacturerModelName (spydcmtk.dcmTools.DicomTags attribute) mergePhaseSeries4D() (in module spydcmtk.dcmVTKTK) mergeSeriesVolumesWithTime() (spydcmtk.dcmTK.DicomStudy method) Modality (spydcmtk.dcmTools.DicomTags attribute)

module spydcmtk spydcmtk.dcmTK spydcmtk.dcmTools spydcmtk.dcmVTKTK spydcmtk.spydcm spydcmtk.spydcm_config MyParser (class in spydcmtk.spydcm)

N

NominalInterval (spydcmtk.dcmTools.DicomTags attribute) NoVtkError

NumberOfAverages (spydcmtk.dcmTools.DicomTags attribute) NumpyEncoder (class in spydcmtk.dcmTools)

O

organiseDicomHeirarchyByUIDs() (in module spydcmtk.dcmTools)

organiseDicoms() (in module spydcmtk.dcmTK) Origin (spydcmtk.dcmVTKTK.PatientMeta property)

P

parseJsonToDictionary() (in module spydcmtk.dcmTools) PatientDateOfBirth (spydcmtk.dcmTools.DicomTags attribute) PatientID (spydcmtk.dcmTools.DicomTags attribute) PatientMeta (class in spydcmtk.dcmVTKTK) PatientName (spydcmtk.dcmTools.DicomTags attribute) PatientOrientation (spydcmtk.dcmTools.DicomTags attribute)

PatientPosition (spydcmtk.dcmTools.DicomTags attribute) (spydcmtk.dcmVTKTK.PatientMeta property) PatientSex (spydcmtk.dcmTools.DicomTags attribute) patientToImageCoordinates() (spydcmtk.dcmVTKTK.PatientMeta method) PixelSpacing (spydcmtk.dcmTools.DicomTags attribute) (spydcmtk.dcmVTKTK.PatientMeta property) printSummaryTable() (spydcmtk.dcmTK.ListOfDicomStudies method)

Q

quit() (spydcmtk.spydcm.INTERACTIVE method)

R

readDicomFile_intoDict() (in module spydcmtk.dcmTools) readImageStackToVTI() (in module spydcmtk.dcmVTKTK) ReceiveCoilName (spydcmtk.dcmTools.DicomTags attribute) removeTimes() (spydcmtk.dcmTK.DicomSeries method) RepetitionTime (spydcmtk.dcmTools.DicomTags attribute)

resetUIDs() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method) returnFirstDicomFound() (in module spydcmtk.spydcm) run() (spydcmtk.spydcm.INTERACTIVE method) runActions() (in module spydcmtk.spydcm)

S

scaleVTI() (in module spydcmtk.dcmVTKTK) SeriesDescription (spydcmtk.dcmTools.DicomTags attribute) SeriesInstanceUID (spydcmtk.dcmTools.DicomTags attribute) SeriesNumber (spydcmtk.dcmTools.DicomTags attribute) seriesNumbersToDicomDirList() (in module spydcmtk.dcmTools) setFromDcmDict() (spydcmtk.dcmTK.ListOfDicomStudies class method) setFromDictionary() (spydcmtk.dcmTK.DicomStudy class method) setFromDirectory() (spydcmtk.dcmTK.DicomSeries class method) (spydcmtk.dcmTK.DicomStudy class method) (spydcmtk.dcmTK.ListOfDicomStudies class method) setFromFileList() (spydcmtk.dcmTK.DicomSeries class method) setFromInput() (spydcmtk.dcmTK.ListOfDicomStudies class method) setFromTar() (spydcmtk.dcmTK.ListOfDicomStudies class method) setFromZip() (spydcmtk.dcmTK.ListOfDicomStudies class method) setMeta() (spydcmtk.dcmVTKTK.PatientMeta method) setSafeNameMode() (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method) setTags_all() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) sliceLoc_InstanceNumberSortKey() (in module spydcmtk.dcmTools) SliceLocation0 (spydcmtk.dcmVTKTK.PatientMeta property) sliceLocations (spydcmtk.dcmTK.DicomSeries property) SliceThickness (spydcmtk.dcmTools.DicomTags attribute) (spydcmtk.dcmVTKTK.PatientMeta property)

SliceVector (spydcmtk.dcmVTKTK.PatientMeta property) SoftwareVersions (spydcmtk.dcmTools.DicomTags attribute) sortByInstanceNumber() (spydcmtk.dcmTK.DicomSeries method) sortBySlice_InstanceNumber() (spydcmtk.dcmTK.DicomSeries method) Spacing (spydcmtk.dcmVTKTK.PatientMeta property) SpacingBetweenSlices (spydcmtk.dcmTools.DicomTags attribute) (spydcmtk.dcmVTKTK.PatientMeta property) spydcmtk module spydcmtk.dcmTK module spydcmtk.dcmTools module spydcmtk.dcmVTKTK module spydcmtk.spydcm module spydcmtk.spydcm_config module streamDicoms() (in module spydcmtk.dcmTools) StudyDate (spydcmtk.dcmTools.DicomTags attribute) StudyDescription (spydcmtk.dcmTools.DicomTags attribute) StudyID (spydcmtk.dcmTools.DicomTags attribute) StudyInstanceUID (spydcmtk.dcmTools.DicomTags attribute) studySummary() (in module spydcmtk.dcmTK)

T

tagsToJson() (spydcmtk.dcmTK.DicomSeries method) Times (spydcmtk.dcmVTKTK.PatientMeta property)

transformVTKData() (spydcmtk.dcmVTKTK.PatientMeta method) TriggerTime (spydcmtk.dcmTools.DicomTags attribute) TriggerWindow (spydcmtk.dcmTools.DicomTags attribute)

U

updateFromMeta() (spydcmtk.dcmVTKTK.PatientMeta method)

V

vtkfilterFlipImageData() (in module spydcmtk.dcmVTKTK)

vtkToHTML() (in module spydcmtk.spydcm)

W

walkdir() (in module spydcmtk.dcmTools) writeArrToVTI() (in module spydcmtk.dcmVTKTK) writeDictionaryToJSON() (in module spydcmtk.dcmTools) writeDirectoryToNII() (in module spydcmtk.dcmTools) (in module spydcmtk.spydcm) writeFDQ() (spydcmtk.dcmTK.DicomStudy method) writeImageStackToDicom() (in module spydcmtk.dcmTK) writeNumpyArrayToDicom() (in module spydcmtk.dcmTK) writeOut_ds() (in module spydcmtk.dcmTools)

writeToNII() (spydcmtk.dcmTK.DicomSeries method) writeToOrganisedFileStructure() (spydcmtk.dcmTK.DicomSeries method) (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method) writeToVTI() (spydcmtk.dcmTK.DicomSeries method) writeToVTS() (spydcmtk.dcmTK.DicomSeries method) writeToZipArchive() (spydcmtk.dcmTK.DicomStudy method) (spydcmtk.dcmTK.ListOfDicomStudies method) writeVTIDict() (in module spydcmtk.dcmVTKTK) writeVTIToDicoms() (in module spydcmtk.dcmTK)

Y

yieldDataset() (spydcmtk.dcmTK.DicomSeries method)